A generalisable head MRI defacing pipeline: Evaluation on 2,566 meningioma scans

TL;DR

This paper introduces a robust, generalisable MRI defacing pipeline that effectively protects patient privacy while maintaining brain anatomy, validated on a large dataset with high success and preservation rates.

Contribution

A novel MRI defacing pipeline combining atlas-based registration and brain masking, demonstrating high success and anatomical preservation on diverse clinical scans.

Findings

99.92% success rate upon visual inspection

Dice similarity coefficient of 0.9975 indicating high anatomical preservation

Validated on 2,566 heterogeneous clinical scans

Abstract

Reliable MRI defacing techniques to safeguard patient privacy while preserving brain anatomy are critical for research collaboration. Existing methods often struggle with incomplete defacing or degradation of brain tissue regions. We present a robust, generalisable defacing pipeline for high-resolution MRI that integrates atlas-based registration with brain masking. Our method was evaluated on 2,566 heterogeneous clinical scans for meningioma and achieved a 99.92 per cent success rate (2,564/2,566) upon visual inspection. Excellent anatomical preservation is demonstrated with a Dice similarity coefficient of 0.9975 plus or minus 0.0023 between brain masks automatically extracted from the original and defaced volumes. Source code is available at https://github.com/cai4cai/defacing_pipeline.